How do I change UV coordinates while the game engine is running?
After another search session, I found the answer here:

For a working blendfile, see the Blenderartists thread, thanks to HG1

from bge import logic # get the controller that executes the script
cont = logic.getCurrentController() # get the object that uses the controller
own = cont.owner     

speed_x = 0.002 # speed by which the coordinates are moved      
speed_y = 0.0   # speed by which the coordinates are moved    
mesh = own.meshes[0] # access the mesh of the object in question    
v_array = mesh.getVertexArrayLength(0) # how many verts are there?      
for v in range(0,v_array): # go through the uv's of every vert
    vert = mesh.getVertex(0,v) 
    uv = vert.getUV()         
    uv[0] += speed_x # change the uv coordinates. uv[0] = x, uv[1] = y
    uv[1] += speed_y        
    vert.setUV(uv) # get the game engine to notice the change!!


The name of your script belongs into the controller.